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Multi-Omics Profiling Identifies Candidate Genes Controlling Seed Size in Peanut

Seed size is the major yield component and a key target trait that is selected during peanut breeding. However, the mechanisms that regulate peanut seed size are unknown. Two peanut mutants with bigger seed size were isolated in this study by (60)Co treatment of a common peanut landrace, Huayu 22, a...

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Autores principales: Liu, Yang, Yi, Congyang, Liu, Qian, Wang, Chunhui, Wang, Wenpeng, Han, Fangpu, Hu, Xiaojun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9740956/
https://www.ncbi.nlm.nih.gov/pubmed/36501316
http://dx.doi.org/10.3390/plants11233276
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author Liu, Yang
Yi, Congyang
Liu, Qian
Wang, Chunhui
Wang, Wenpeng
Han, Fangpu
Hu, Xiaojun
author_facet Liu, Yang
Yi, Congyang
Liu, Qian
Wang, Chunhui
Wang, Wenpeng
Han, Fangpu
Hu, Xiaojun
author_sort Liu, Yang
collection PubMed
description Seed size is the major yield component and a key target trait that is selected during peanut breeding. However, the mechanisms that regulate peanut seed size are unknown. Two peanut mutants with bigger seed size were isolated in this study by (60)Co treatment of a common peanut landrace, Huayu 22, and were designated as the “big seed” mutant lines (hybs). The length and weight of the seed in hybs were about 118% and 170% of those in wild-type (WT), respectively. We adopted a multi-omics approach to identify the genomic locus underlying the hybs mutants. We performed whole genome sequencing (WGS) of WT and hybs mutants and identified thousands of large-effect variants (SNPs and indels) that occurred in about four hundred genes in hybs mutants. Seeds from both WT and hybs lines were sampled 20 days after flowering (DAF) and were used for RNA-Seq analysis; the results revealed about one thousand highly differentially expressed genes (DEGs) in hybs compared to WT. Using a method that combined large-effect variants with DEGs, we identified 45 potential candidate genes that shared gene product mutations and expression level changes in hybs compared to WT. Among the genes, two candidate genes encoding cytochrome P450 superfamily protein and NAC transcription factors may be associated with the increased seed size in hybs. The present findings provide new information on the identification and functional research into candidate genes responsible for the seed size phenotype in peanut.
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spelling pubmed-97409562022-12-11 Multi-Omics Profiling Identifies Candidate Genes Controlling Seed Size in Peanut Liu, Yang Yi, Congyang Liu, Qian Wang, Chunhui Wang, Wenpeng Han, Fangpu Hu, Xiaojun Plants (Basel) Article Seed size is the major yield component and a key target trait that is selected during peanut breeding. However, the mechanisms that regulate peanut seed size are unknown. Two peanut mutants with bigger seed size were isolated in this study by (60)Co treatment of a common peanut landrace, Huayu 22, and were designated as the “big seed” mutant lines (hybs). The length and weight of the seed in hybs were about 118% and 170% of those in wild-type (WT), respectively. We adopted a multi-omics approach to identify the genomic locus underlying the hybs mutants. We performed whole genome sequencing (WGS) of WT and hybs mutants and identified thousands of large-effect variants (SNPs and indels) that occurred in about four hundred genes in hybs mutants. Seeds from both WT and hybs lines were sampled 20 days after flowering (DAF) and were used for RNA-Seq analysis; the results revealed about one thousand highly differentially expressed genes (DEGs) in hybs compared to WT. Using a method that combined large-effect variants with DEGs, we identified 45 potential candidate genes that shared gene product mutations and expression level changes in hybs compared to WT. Among the genes, two candidate genes encoding cytochrome P450 superfamily protein and NAC transcription factors may be associated with the increased seed size in hybs. The present findings provide new information on the identification and functional research into candidate genes responsible for the seed size phenotype in peanut. MDPI 2022-11-28 /pmc/articles/PMC9740956/ /pubmed/36501316 http://dx.doi.org/10.3390/plants11233276 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Liu, Yang
Yi, Congyang
Liu, Qian
Wang, Chunhui
Wang, Wenpeng
Han, Fangpu
Hu, Xiaojun
Multi-Omics Profiling Identifies Candidate Genes Controlling Seed Size in Peanut
title Multi-Omics Profiling Identifies Candidate Genes Controlling Seed Size in Peanut
title_full Multi-Omics Profiling Identifies Candidate Genes Controlling Seed Size in Peanut
title_fullStr Multi-Omics Profiling Identifies Candidate Genes Controlling Seed Size in Peanut
title_full_unstemmed Multi-Omics Profiling Identifies Candidate Genes Controlling Seed Size in Peanut
title_short Multi-Omics Profiling Identifies Candidate Genes Controlling Seed Size in Peanut
title_sort multi-omics profiling identifies candidate genes controlling seed size in peanut
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9740956/
https://www.ncbi.nlm.nih.gov/pubmed/36501316
http://dx.doi.org/10.3390/plants11233276
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